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- PDB-8ct0: Crystal structure of FAD reductase CtcQ from Kitasatospora aureof... -

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Basic information

Entry
Database: PDB / ID: 8ct0
TitleCrystal structure of FAD reductase CtcQ from Kitasatospora aureofaciens in complex with FAD and NAD
ComponentsFlavin reductase (NADH)Flavin reductase (NADH)
KeywordsFLAVOPROTEIN / Reductase / Chlortetracycline / FAD binding / Biosysthesis / Natural product
Function / homology
Function and homology information


flavin reductase (NADH) / flavin reductase (NADH) activity / FMN binding
Similarity search - Function
Flavin reductase like domain / Flavin reductase like domain / Flavin reductase like domain / FMN-binding split barrel
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / PHOSPHATE ION / Flavin reductase (NADH)
Similarity search - Component
Biological speciesKitasatospora aureofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsHou, C. / Tsodikov, O.V.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Crystal structures and complex formation of halogenase CtcP and FAD reductase CtcQ from the chlortetracycline biosynthetic pathway
Authors: Hou, C. / Garneau-Tsodikova, S. / Tsodikov, O.V.
History
DepositionMay 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flavin reductase (NADH)
B: Flavin reductase (NADH)
C: Flavin reductase (NADH)
D: Flavin reductase (NADH)
E: Flavin reductase (NADH)
F: Flavin reductase (NADH)
G: Flavin reductase (NADH)
H: Flavin reductase (NADH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,36936
Polymers167,9038
Non-polymers13,46628
Water4,234235
1
A: Flavin reductase (NADH)
F: Flavin reductase (NADH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4039
Polymers41,9762
Non-polymers3,4277
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10290 Å2
ΔGint-108 kcal/mol
Surface area13620 Å2
MethodPISA
2
B: Flavin reductase (NADH)
H: Flavin reductase (NADH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2839
Polymers41,9762
Non-polymers3,3077
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10320 Å2
ΔGint-105 kcal/mol
Surface area13740 Å2
MethodPISA
3
C: Flavin reductase (NADH)
G: Flavin reductase (NADH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2819
Polymers41,9762
Non-polymers3,3057
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10360 Å2
ΔGint-108 kcal/mol
Surface area13650 Å2
MethodPISA
4
D: Flavin reductase (NADH)
E: Flavin reductase (NADH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4039
Polymers41,9762
Non-polymers3,4277
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10590 Å2
ΔGint-105 kcal/mol
Surface area13540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.739, 123.598, 102.698
Angle α, β, γ (deg.)90.000, 99.100, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Flavin reductase (NADH) / Flavin reductase (NADH)


Mass: 20987.883 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: The C-terminal sequence LEHHHHHH is a C-terminal tag artifact. The residues are not present in the structure due to disorder.
Source: (gene. exp.) Kitasatospora aureofaciens (bacteria) / Gene: ctcQ, B6264_18520, HS99_0013300 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: S4S3E3, flavin reductase (NADH)

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Non-polymers , 5 types, 263 molecules

#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#5: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.92 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.6 M KH2PO4,0.6 M NaH2PO4, 0.1 M Tris pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 49072 / % possible obs: 96.4 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / CC1/2: 0.978 / Rmerge(I) obs: 0.138 / Net I/σ(I): 8.9
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.568 / Num. unique obs: 2399 / CC1/2: 0.696 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L82

4l82


Resolution: 2.45→34.97 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.877 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.112 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2557 2512 5.1 %RANDOM
Rwork0.1935 ---
obs0.1967 46528 95.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.59 Å2 / Biso mean: 21.327 Å2 / Biso min: 2.94 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å20 Å20.63 Å2
2---1.36 Å2-0 Å2
3---2.18 Å2
Refinement stepCycle: final / Resolution: 2.45→34.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10011 0 847 235 11093
Biso mean--26.84 21.29 -
Num. residues----1378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01311155
X-RAY DIFFRACTIONr_bond_other_d0.0350.01710205
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.65215415
X-RAY DIFFRACTIONr_angle_other_deg2.3291.5723506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.44951367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.50519.083447
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.878151449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0081598
X-RAY DIFFRACTIONr_chiral_restr0.0510.21459
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212320
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022299
LS refinement shellResolution: 2.45→2.513 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 178 -
Rwork0.249 2914 -
all-3092 -
obs--81.84 %

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